WOLFRAM SYSTEM MODELER
This is a placeholder model. It requires the BioChem library.
The following documentation is taken from the main example of the downloadable model. Once you have downloaded all the model dependencies, the model can be downloaded here.
This model illustrates the functions of an allosteric enzyme, aspartate carbamoyltransferase (ATCase), and how its activity is affected both by negative feedback regulation and pure modifiers.
In order to get the full experience of this example, you need the following:
These pages show an overview of the example. For the full example, open the accompanying notebook AllostericControl.nb.
The example model consists of the vital substances in the ATCase reaction. Aspartate and carbamoyl phosphate react in an allosterically catalyzed reaction to become carbamoyl aspartate and phosphate. Carbamoyl aspartate is then further transformed into cytidine triphosphate (CTP), in a reaction that in reality consists of several steps that here have been condensed into one. CTP then, together with uridine triphosphate (UTP), inhibits the reaction and decreases the reaction rate by favoring the tense state of ATCase. Adenosine triphosphate (ATP) counters this by instead favoring the relaxed state.
Simulating the model allows you to look at how the different substances change over time, and how they are affected by each other. In order to properly analyze this model, it is recommended to use the Wolfram Language notebook that came with this model when it was downloaded. If you prefer to analyze the model in SystemModeler, then follow the guide below.
When the simulation is finished and Simulation Center has been opened, you can analyze the result by clicking the various states to the left of the Simulation Center window and selecting the proper value to analyze, for example, Aspartate.c for changes in aspartate concentration over time or ATCase.der for changes in the derivative of ATCase over time.
To analyze the model based on a different initial parameter set than the default, select the state you want to edit in the Model Center and change the desired initial value under Initialization in the General tab. It can also be done directly from Simulation Center, under the Variables tab.
This domain example is an informational resource made freely available by Wolfram Research.
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